Fig. 8: MAIT cells are activated by and exert cytotoxicity against macrophages infected with SARS-CoV-2.

a,b, t-SNE analysis of scRNA-seq of MAIT cells sorted from uninfected controls (n = 4; 13,043 MAIT cells) and patients with COVID-19 in the ICU (n = 4; 8,832 MAIT cells). Each color indicates a different condition (uninfected or ICU; a) or a unique patient (b). c, t-SNE analysis representing the log₂ fold change in the expression of GNLY, PRDM1, PRF1, CD69, TXNIP, NFKBIA and IFITM1 between uninfected controls and patients with COVID-19 in the ICU (n = 4 for each group). d, Relative mRNA levels of PRDM1, HOBIT and TBX21 from sorted CD161⁺Va7.2⁺ MAIT cells from patients with COVID-19 admitted to an IDU (n = 9) and ICU (n = 9). e, Representative mean fluorescence intensity of GzB expression in MAIT cells from one healthy donor, cocultured for 4 d with either uninfected or SARS-CoV-2-infected macrophages (MOI of 3) and supplemented or not with anti-MR1. f–h, Representative quantile contour plots and frequencies of CD69⁺ and CD107a⁺ MAIT cells (gated on total MAIT cells) after coculture for 4 d with either uninfected or SARS-CoV-2-infected macrophages (MOI of 3) and supplemented or not with anti-MR1 (n = 9 replicates from three donors). RT–qPCR results were normalized to the expression of the reference housekeeping 18S gene (d). Small horizontal lines indicate the median. Each symbol represents one patient (d) or one replicate (g and h). *P < 0.05, **P < 0.01 and ****P < 0.0001 (two-sided Mann–Whitney non-parametric test (d) and Wilcoxon signed-rank test (g and h)).